Merge pull request #156 from StingraySoftware/polarimetric_lcs

Generic lcs

.github/workflows/ci_test.yml

@@ -14,17 +14,85 @@ env:
   TOXARGS: '-v'
 
 jobs:
-  ci-tests:
-    name: ${{ matrix.os }}, ${{ matrix.tox_env }}
+
+  check_commit:
+    # Check the commit message for the presence of keywords that indicate
+    # that the CI tests should be skipped, in favor of running doc builds only.
+    # Messages like [docs only], [docs-only], or [skip-tests] will skip
+    # Only the CI part of the workflow, not the doc build.
+    # [skip ci], [ci skip] etc. are instead handled by GitHub itself and will skip
+    # the entire workflow.
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      # Found this solution at
+      # https://monadical.com/posts/filters-github-actions.html#Case-2-Pull-request
+      - name: check if message indicates that tests should be skipped
+        id: check_commit
+        run: |
+          message=$(git log -1 --pretty=format:'%B')
+          re="\[(docs.only|skip-tests).*\]"
+          if [[ $message =~ $re ]]; then
+            echo "match=true" >> $GITHUB_OUTPUT
+            echo "$message -> Match is true"
+          else
+            echo "$message -> Match is false"
+          fi
+    outputs:
+      match: ${{ steps.check_commit.outputs.match }}
+
+  docs-tests:
+    name: ${{ matrix.tox_env }}
     runs-on: ${{ matrix.os }}
-    if: "!(contains(github.event.head_commit.message, '[skip ci]') || contains(github.event.head_commit.message, '[ci skip]'))"
     strategy:
       fail-fast: false
       matrix:
         include:
           - os: ubuntu-latest
-            python: '3.8'
+            python: '3.10'
             tox_env: 'build_docs'
+          - os: ubuntu-latest
+            python: '3.10'
+            tox_env: 'linkcheck'
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+      - name: Check out that no sensitive environment variable is shared
+        run: env
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Install base dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox
+      - name: Install system dependencies
+        run: sudo apt-get -y install graphviz pandoc
+      - name: Print Python, pip, setuptools, and tox versions
+        run: |
+          python -c "import sys; print(f'Python {sys.version}')"
+          python -c "import pip; print(f'pip {pip.__version__}')"
+          python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
+          python -c "import tox; print(f'tox {tox.__version__}')"
+      - name: Run tests
+        run: tox -e ${{ matrix.tox_env }}
+
+  ci-tests:
+    needs: check_commit
+    if: ${{ needs.check_commit.outputs.match != 'true' }}
+    name: ${{ matrix.os }}, ${{ matrix.tox_env }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
           - os: ubuntu-latest
             python: '3.10'
             tox_env: 'codestyle'

CITATION

@@ -15,7 +15,7 @@ howpublished = {Astrophysics Source Code Library},
     month = feb,
 archivePrefix = "ascl",
    eprint = {1502.021},
-   adsurl = {http://adsabs.harvard.edu/abs/2015ascl.soft02021B},
+   adsurl = {https://adsabs.harvard.edu/abs/2015ascl.soft02021B},
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
@@ -39,7 +39,7 @@ archivePrefix = "arXiv",
       eid = {109},
     pages = {109},
       doi = {10.1088/0004-637X/800/2/109},
-   adsurl = {http://adsabs.harvard.edu/abs/2015ApJ...800..109B},
+   adsurl = {https://adsabs.harvard.edu/abs/2015ApJ...800..109B},
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 

CODE_OF_CONDUCT.md

@@ -40,7 +40,7 @@ Project maintainers who do not follow or enforce the Code of Conduct in good fai
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://contributor-covenant.org/version/1/4][version]
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+[homepage]: https://contributor-covenant.org
+[version]: https://contributor-covenant.org/version/1/4/

CONTRIBUTING.md

@@ -1,8 +1,8 @@
 Contributions from everyone, experienced and inexperienced, are welcome!
 If you don't know where to start, look at the open [Issues](https://github.com/StingraySoftware/HENDRICS/issues)
-and/or get involved in our [Slack channel ](http://slack-invite.timelabtechnologies.com/).
+and/or get involved in our [Slack channel ](https://join.slack.com/t/stingraysoftware/shared_invite/zt-49kv4kba-mD1Y~s~rlrOOmvqM7mZugQ).
 
-Please follow the [Astropy contribution guidelines](http://docs.astropy.org/en/stable/development/workflow/development_workflow.html),
-and the [Astropy coding guidelines](http://docs.astropy.org/en/stable/development/codeguide.html#coding-style-conventions).
+Please follow the [Astropy contribution guidelines](https://docs.astropy.org/en/stable/development/workflow/development_workflow.html),
+and the [Astropy coding guidelines](https://docs.astropy.org/en/stable/development/codeguide.html#coding-style-conventions).
 This code is written in Python 3.8+
 Tests run at each commit during Pull Requests, so it is easy to single out points in the code that break this compatibility.

README.rst

@@ -18,7 +18,7 @@ difficult to treat power density spectra with the usual tools. By
 exploiting the presence of two independent detectors, one could use the
 **cospectrum** as a proxy for the power density spectrum (for an
 explanation of why this is important, look at Bachetti et al., *ApJ*,
-800, 109 -`arXiv:1409.3248 <http://arxiv.org/abs/1409.3248>`__).
+800, 109 -`arXiv:1409.3248 <https://arxiv.org/abs/1409.3248>`__).
 
 Today, this set of command line scripts is much more complete and it is
 capable of working with the data of many more satellites. Among the
@@ -34,18 +34,17 @@ users will have the choice to analyze single datasets with an easy
 interactive interface, and continue the analysis in batch mode with
 HENDRICS. The periodograms produced by HENDRICS (like a power density
 spectrum or a cospectrum), can be saved in a format compatible with
-`Xspec <http://heasarc.gsfc.nasa.gov/xanadu/xspec/>`__ or
-`Isis <http://space.mit.edu/home/mnowak/isis_vs_xspec/mod.html>`__, for
+``XSpec`` or ``ISIS``, for
 those who are familiar with those fitting packages. Despite its original
 main focus on NuSTAR, the software can be used to make standard
 aperiodic timing analysis on X-ray data from, in principle, any other
 satellite (for sure XMM-Newton and RXTE).
 
 The **documentation** can be found
-`here <http://hendrics.readthedocs.io>`__.
+`here <https://hendrics.readthedocs.io>`__.
 
 A **tutorial** is also available
-`here <http://hendrics.readthedocs.io/en/main/tutorials/index.html>`__.
+`here <https://hendrics.readthedocs.io/en/main/tutorials/index.html>`__.
 
 Installation instructions
 -------------------------
@@ -74,13 +73,13 @@ license information in the ``LICENSE.rst`` file.
 **If you use this software in a publication**, please refer to its
 Astrophysics Source Code Library identifier:
 
-1. Bachetti, M. 2018, HENDRICS: High ENergy Data Reduction Interface from the Command Shell, record `ascl:1805.019 <http://ascl.net/1805.019>`__.
+1. Bachetti, M. 2018, HENDRICS: High ENergy Data Reduction Interface from the Command Shell, record `ascl:1805.019 <https://ascl.net/1805.019>`__.
 
 and please also cite `stingray <https://stingray.science/stingray/citing.html>`
 
 In particular, **if you use the cospectrum**, please also refer to:
 
-2. Bachetti et al. 2015, `ApJ <http://iopscience.iop.org/0004-637X/800/2/109/>`__ , **800**, 109.
+2. Bachetti et al. 2015, `ApJ <https://iopscience.iop.org/0004-637X/800/2/109/>`__ , **800**, 109.
 
 If you have found a bug please report it by creating a
 new issue on the `HENDRICS GitHub issue tracker. <https://github.com/StingraySoftware/HENDRICS/issues>`_
@@ -89,7 +88,7 @@ Development guidelines
 ----------------------
 
 Please follow the development workflow for
-`the Astropy project <http://docs.astropy.org/en/stable/development/workflow/development_workflow.html>`__.
+`the Astropy project <https://docs.astropy.org/en/stable/development/workflow/development_workflow.html>`__.
 In the hendrics/tests
 directory, there is a test suite called ``test_fullrun.py``. These tests
 use the actual command line scripts, and should always pass (albeit with
@@ -99,6 +98,6 @@ the API.
 .. |Build Status| image:: https://github.com/StingraySoftware/HENDRICS/workflows/CI%20Tests/badge.svg
     :target: https://github.com/StingraySoftware/HENDRICS/actions/
 .. |Coverage Status| image:: https://codecov.io/gh/StingraySoftware/HENDRICS/branch/main/graph/badge.svg
-  :target: https://codecov.io/gh/StingraySoftware/HENDRICS
+  :target: https://app.codecov.io/gh/StingraySoftware/HENDRICS
 .. |Documentation Status| image:: https://readthedocs.org/projects/hendrics/badge/?version=main
-   :target: http://hendrics.readthedocs.io/en/main/?badge=main
+   :target: https://hendrics.readthedocs.io/en/main/?badge=main

docs/index.rst

@@ -13,9 +13,9 @@ HENDRICS documentation
 .. |Build Status| image:: https://github.com/StingraySoftware/HENDRICS/workflows/CI%20Tests/badge.svg
     :target: https://github.com/StingraySoftware/HENDRICS/actions/
 .. |Coverage Status| image:: https://codecov.io/gh/StingraySoftware/HENDRICS/branch/main/graph/badge.svg
-  :target: https://codecov.io/gh/StingraySoftware/HENDRICS
+  :target: https://app.codecov.io/gh/StingraySoftware/HENDRICS
 .. |Documentation Status| image:: https://readthedocs.org/projects/hendrics/badge/?version=main
-   :target: http://hendrics.readthedocs.io/en/main/?badge=main
+   :target: https://hendrics.stingray.science/en/main/?badge=main
 
 Description
 -----------
@@ -34,8 +34,7 @@ users will have the choice to analyze single datasets with an easy
 interactive interface, and continue the analysis in batch mode with
 HENDRICS. The periodograms produced by HENDRICS (like a power density
 spectrum or a cospectrum), can be saved in a format compatible with
-`Xspec <http://heasarc.gsfc.nasa.gov/xanadu/xspec/>`__ or
-`Isis <http://space.mit.edu/home/mnowak/isis_vs_xspec/mod.html>`__, for
+``XSpec`` or ``ISIS``, for
 those who are familiar with those fitting packages. Despite its original
 main focus on NuSTAR, the software can be used to make standard
 aperiodic timing analysis on X-ray data from, in principle, any other
@@ -50,11 +49,14 @@ HENDRICS 8.0 (under development)
 + ``HENaccelsearch`` now has additional options for detrending, denoising and deorbiting
 + An improved Maximum likelihood algorithm as FFTFIT substitute for TOA calculation
 + NASA's IXPE added to supported missions
++ Compatible with `Stingray 1.1 <https://github.com/StingraySoftware/stingray/releases/tag/v1.1>`__ or newer
++ Add option to obtain weighted light curves
+
 
 HENDRICS 7.0
 ~~~~~~~~~~~~
 
-+ Based on `Stingray 1.0 <https://github.com/StingraySoftware/stingray/releases/tag/v1.>`__, bringing a huge bump in performance
++ Based on `Stingray 1.0 <https://github.com/StingraySoftware/stingray/releases/tag/v1.0>`__, bringing a huge bump in performance
 + Following Astropy, Numpy and Scipy, HENDRICS 7.0 is only compatible with Python >3.8
 + Accepts many more file formats for round-trip of Stingray objects, thanks to the new functionality of Stingray.
 + Energy-filtered periodograms
@@ -114,7 +116,7 @@ Functionality additions:
 .. Note ::
 
     MaLTPyNT provisionally accepted as an
-    `Astropy affiliated package <http://www.astropy.org/affiliated/index.html>`__
+    `Astropy affiliated package <https://www.astropy.org/affiliated/index.html>`__
 
 
 In preparation for the 2.0 release, the API has received some visible changes.
@@ -176,13 +178,13 @@ license information in the ``LICENSE.rst`` file.
 **If you use this software in a publication**, please refer to its
 Astrophysics Source Code Library identifier:
 
-1. Bachetti, M. 2018, HENDRICS: High ENergy Data Reduction Interface from the Command Shell, record `ascl:1805.019 <http://ascl.net/1805.019>`__.
+1. Bachetti, M. 2018, HENDRICS: High ENergy Data Reduction Interface from the Command Shell, record `ascl:1805.019 <https://ascl.net/1805.019>`__.
 
 and please also cite `stingray <https://stingray.science/stingray/citing.html>`
 
 In particular, **if you use the cospectrum**, please also refer to:
 
-2. Bachetti et al. 2015, `ApJ <http://iopscience.iop.org/0004-637X/800/2/109/>`__ , **800**, 109.
+2. Bachetti et al. 2015, `ApJ <https://iopscience.iop.org/article/10.1088/0004-637X/800/2/109>`__ , **800**, 109.
 
 If you have found a bug please report it by creating a
 new issue on the `HENDRICS GitHub issue tracker. <https://github.com/StingraySoftware/HENDRICS/issues>`_
@@ -193,15 +195,15 @@ Acknowledgements
 (MaLTPyNT) 2.0
 ~~~~~~~~~~~~~~
 I would like to thank all the co-authors of `the NuSTAR timing
-paper <http://arxiv.org/abs/1409.3248>`__ and the NuSTAR X-ray binaries
+paper <https://arxiv.org/abs/1409.3248>`__ and the NuSTAR X-ray binaries
 working group. This software would not exist without the interesting
 discussions before and around that paper. In particular, I would like to
 thank Ivan Zolotukhin, Francesca Fornasini, Erin Kara, Felix Fürst,
 Poshak Gandhi, John Tomsick and Abdu Zoghbi for helping testing the code
 and giving various suggestions on how to improve it. Last but not least,
 I would like to thank Marco Buttu (by the way, `check out his book if
 you speak
-Italian <http://www.amazon.it/Programmare-con-Python-completa-DigitalLifeStyle-ebook/dp/B00L95VURC/ref=sr_1_1?s=books&ie=UTF8&qid=1424298092&sr=1-1>`__)
+Italian <https://www.amazon.it/Programmare-con-Python-completa-DigitalLifeStyle-ebook/dp/B00L95VURC/ref=sr_1_1?s=books&ie=UTF8&qid=1424298092&sr=1-1>`__)
 for his priceless pointers on Python coding and code management
 techniques.
 
@@ -229,8 +231,6 @@ API documentation
    :maxdepth: 2
 
    hendrics/modules
-   hendrics/index
-
 
 Indices and tables
 ==================

docs/install.rst

@@ -7,41 +7,41 @@ Prerequisites
 You'll need a recent python 3.8+ installation.
 The main dependency is
 
-1. `Stingray <http://github.com/stingraysoftware/stingray>`__,
+1. `Stingray <https://github.com/stingraysoftware/stingray>`__,
 
 which in turn depends on
 
-2. `Numpy <http://www.numpy.org/>`__;
+2. `Numpy <https://www.numpy.org/>`__;
 
-3. `Matplotlib <http://matplotlib.org/>`__;
+3. `Matplotlib <https://matplotlib.org/>`__;
 
-4. `Scipy <http://scipy.org/>`__;
+4. `Scipy <https://scipy.org/>`__;
 
-5. `Astropy <http://www.astropy.org/>`__
+5. `Astropy <https://www.astropy.org/>`__
 
 **Optional but recommended** dependencies are:
 
-6. the `netCDF 4 library <http://www.unidata.ucar.edu/software/netcdf/>`__ with its
+6. the `netCDF 4 library <https://www.unidata.ucar.edu/software/netcdf/>`__ with its
 `python bindings <https://github.com/Unidata/netcdf4-python>`__;
 
-7. `Numba <http://numba.pydata.org>`__;
+7. `Numba <https://numba.pydata.org>`__;
 
-8. `statsmodels <http://www.statsmodels.org/stable/index.html>`__
+8. `statsmodels <https://www.statsmodels.org/stable/index.html>`__
 
-9. `emcee <http://dfm.io/emcee/current/>`__
+9. `emcee <https://emcee.readthedocs.io/en/stable/>`__
 
-10. `pint <http://github.com/nanograv/pint/>`__
+10. `pint <https://github.com/nanograv/pint/>`__
 
 You should also
-have a working `HEASoft <http://heasarc.nasa.gov/lheasoft/>`__
+have a working `HEASoft <https://heasarc.gsfc.nasa.gov/lheasoft/>`__
 installation to produce the cleaned event files and to use
-`XSpec <http://heasarc.nasa.gov/lheasoft/xanadu/xspec/index.html>`__.
+`XSpec <https://heasarc.gsfc.nasa.gov/xanadu/xspec/>`__.
 
 Installing releases
 -------------------
 ::
 
-    $ pip install hendrics numba emcee statsmodels netcdf4 matplotlib stingray>=1.0b1
+    $ pip install hendrics numba emcee statsmodels netcdf4 matplotlib stingray>=1.1
 
 
 Installing the Development version